The immune system is never at rest, nor is it ever isolated from its environment. It is in constant interaction with myriads of microbes which can be pathogenic, commensal or mutualistic. 

A host has two ways to defend itself against pathogens: it can clear the microbe (resistance) or reduce its impact (tolerance). Resistance mechanisms protect the infected host by reducing its pathogen burden and is a function of the immune system which works by detection, destruction or expulsion of pathogens. In this case, both innate and adaptive immune systems contribute to host resistance to infections. Tolerance is a host defence strategy that traduces the negative impact of infections on host fitness, ultimately by decreasing the host susceptibility to tissue damage.

Recent work has shed light on the impact of commensal and mutualistic microbes on the development, induction, training and functioning of the immune system. I will describe here some examples in which microbiota and immune systems can have a love and hate relationship.